In some portions of nuclear piping systems, stratification phenomena may occur due to the density difference between hot and cold stream. When the temperature difference is large, the stratified flow under diverse operating conditions can produce high thermal stress, which leads to unanticipated piping integrity issues. The objectives of this research are to examine controvertible numerical factors such as model size, grid resolution, turbulent parameters, governing equation, inflow direction and pipe wall. Parametric three-dimensional computational fluid dynamics analyses were carried out to quantify effects of these parameters on the accuracy of temperature profiles in a typical nuclear piping with complex geometries. Then, as a key finding, it was recommended to use optimized mesh of real piping with the conjugated heat transfer condition for accurate thermal stratification analyses.